Revision: 20167
http://sourceforge.net/p/jmol/code/20167
Author: hansonr
Date: 2014-12-19 15:09:21 +0000 (Fri, 19 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.19"
bug fix: JavaScript connect broken
due to j2s failure to create bsAromatic when BondCollection created
(14.3.7)
due to j2s bug in instantiating global definitions in super classes
using Clazz_prepareFields
bug fix: label, echo, and measurement text should not display when deeper
than zSlab with zShade is TRUE
bug fix: mmCIF reader load filter biomolecule 1
broken for viruses with symmetry ranges listed as "1-60" with a hyphen
bug fix: mmCIF reader coarse-grain load filter bysymop broken
bug fix: mmCIF reader coarse-grain load filter bychain broken
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2014-12-19
14:16:33 UTC (rev 20166)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2014-12-19
15:09:21 UTC (rev 20167)
@@ -73,9 +73,6 @@
abstract public class AtomCollection {
- private static final Float MINUSZERO = Float.valueOf(-0.0f);
-
-
public Viewer vwr;
protected GData g3d;
@@ -831,7 +828,7 @@
if (Float.isNaN(partialCharge))
return false;
if (partialCharges == null) {
- if (partialCharge == 0 &&
!Float.valueOf(partialCharge).equals(MINUSZERO))
+ if (partialCharge == 0)
return false; // no need to store a 0.
partialCharges = new float[at.length];
}
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2014-12-19
14:16:33 UTC (rev 20166)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2014-12-19
15:09:21 UTC (rev 20167)
@@ -62,6 +62,9 @@
protected final static int MAX_BONDS_LENGTH_TO_CACHE = 5;
protected final static int MAX_NUM_TO_CACHE = 200;
+ // J2S note 12/19/2014: J2S fails to instantiate fields for superclasses
such as this
+ // thus, using protected bsAromatic = new BS(); fails
+
protected void setupBC() {
bsAromatic = new BS();
numCached = new int[MAX_BONDS_LENGTH_TO_CACHE];
Modified: trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2014-12-19 14:16:33 UTC (rev 20166)
+++ trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2014-12-19 15:09:21 UTC (rev 20167)
@@ -37,6 +37,7 @@
import javajs.util.P3;
import javajs.util.P3i;
+import javajs.util.PT;
import javajs.util.T3;
import javajs.util.V3;
@@ -63,10 +64,8 @@
return renderIso();
}
- protected boolean renderIso() {
-
+ protected boolean renderIso() {
setGlobals();
-
for (int i = isosurface.meshCount; --i >= 0;) {
mesh = imesh = (IsosurfaceMesh) isosurface.meshes[i];
if (imesh.connections != null &&
!vwr.ms.at[imesh.connections[0]].checkVisible())
@@ -166,7 +165,7 @@
&& imesh.jvxlData.isSlabbable) {
P3[] points = imesh.jvxlData.boundingBox;
float z0 = Float.MAX_VALUE;
- float z1 = Float.MIN_VALUE;
+ float z1 = PT.FLOAT_MIN_SAFE;
for (int i = points.length; --i >= 0;) {
pt2f.setT(points[i]);
tm.transformPt3f(pt2f, pt2f);
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